Stabilized reverse transcriptase fustion proteins

ABSTRACT

Stabilized reverse transcriptase fusion proteins including a thermostable reverse transcriptase connected to a stabilizer protein are described. Attaching the stabilizer protein to the thermostable reverse transcriptase stabilizes the fusion protein and can aid in its purification, provide increased solubility, allow for longer storage, or allow the fusion protein to be used under more rigorous conditions such as higher temperature. The stabilized reverse transcriptase fusion protein can also include a linker between the stabilizer protein and the thermostable reverse temperature. The stabilized reverse transcriptase fusion proteins are suitable for use in nucleic acid amplification methods such as the reverse transcription polymerase chain reaction and other applications involving cDNA synthesis.

CONTINUING APPLICATION DATA

This application claims the benefit of U.S. Provisional Application Ser.No. 61/157,332, filed Mar. 4, 2009, which is incorporated by referenceherein.

GOVERNMENT FUNDING

This work was supported, at least in part, by grant number GM37949-22from the Department of Health and Human Services, National Institutes ofHealth. The United States government may have certain rights in thisinvention.

BACKGROUND OF THE INVENTION

Reverse transcription polymerase chain reaction, abbreviated as RT-PCR,is a well known technique for amplifying RNA. In RT-PCR, an RNA strandis reverse transcribed into complementary DNA (cDNA), which is thenamplified using DNA polymerase in the polymerase chain reaction. In thefirst step of this process, cDNA is made from an RNA template usingdeoxyribonucleotide phosphates and reverse transcriptase together with aDNA primer.

Synthesis of cDNA from the RNA template can be hindered by RNA secondaryand tertiary structures, which consist of helices and various otherkinds of kinks in the RNA strand. RNA secondary and tertiary structurecan be decreased by carrying out the reaction at a higher temperature(e.g., above 50° C.) or by adding denaturing additives. However, theaddition of denaturing additives is undesirable because it often reducesreverse transcriptase activity. Higher temperatures also provide theadvantage of increasing the specificity of DNA synthesis by decreasingnon-specific primer binding. Unfortunately, only a limited number ofreverse transcriptases capable of operating at high temperature arecurrently available, and these exhibit relatively low fidelity DNApolymerization. For example, commercially available Avian MyeloblastosisVirus reverse transcriptase includes RNase H activity and can functionat 37° C., but has a fidelity of only about 1.7×10⁻⁴. RNase H activitycompetes with the DNA polymerase activity and the primer binding siteand, therefore, cDNA yield is lower. Accordingly, there is a need forreverse transcriptase enzymes that are able to carry out reversetranscription at higher temperatures, including those that have highfidelity and processivity. Such enzymes are beneficial because highertemperatures decrease obstructing RNA secondary and tertiary structureand increase the specificity of reverse transcription by allowing theuse of longer and more specific primers.

SUMMARY OF THE INVENTION

In one aspect, the invention provides a stabilized reverse transcriptase(RT) fusion protein that includes a thermostable reverse transcriptaseconnected to a stabilizer protein. In one embodiment of the stabilizedreverse transcriptase fusion protein, the thermostable reversetranscriptase is a bacterial reverse transcriptase. In a furtherembodiment, the bacterial reverse transcriptase is a group IIintron-derived reverse transcriptase. Examples of thermostable bacterialreverse transcriptases include Thermosynechococcus elongatus reversetranscriptase and Geobacillus stearothermophilus reverse transcriptase.In another embodiment, the thermostable reverse transcriptase exhibitshigh fidelity cDNA synthesis. In yet another embodiment, thethermostable reverse transcriptase includes a polypeptide with an aminoacid sequence identity that is substantially similar to a sequenceselected from the group consisting of SEQ ID NO: 1. SEQ ID NO: 2, SEQ IDNO: 3. SEQ ID NO: 4, or SEQ ID NO: 5.

The stabilized reverse transcriptase fusion protein includes astabilizer protein that, when linked to the reverse transcriptase,enhances the shelf life and/or the thermal stability and/or thesolubility of the thermostable reverse transcriptase. In certainembodiments, the stabilizer protein is an affinity protein or asolubility-enhancing protein (e.g., a maltose binding protein orN-utilization substance A protein). In additional embodiments, thestabilizer protein is modified by replacing certain charged amino acidswith uncharged amino acids.

The stabilized reverse transcriptase fusion protein can also include alinker peptide that connects the thermostable reverse transcriptase tothe stabilizer protein. In some embodiments, this linker peptide is anon-cleavable linker, while in other embodiments it is a non-cleavablerigid linker. In some embodiments, the linker peptide consists of 1 to20 amino acids, while in other embodiments the linker peptide consistsof 1 to 5 or 3 to 5 amino acids. For example, a rigid non-cleavablelinker peptide can include 5 alanine amino acids.

In additional embodiments, the stabilized reverse transcriptase fusionprotein has an amino acid sequence that includes a polypeptide with anamino acid sequence identity that is substantially similar to a sequenceselected from the group consisting of SEQ ID NO: 6, SEQ ID NO: 7, SEQ IDNO: 8, SEQ ID NO: 9, or SEQ ID NO: 10. In some embodiments, thestabilized reverse transcriptase fusion protein is a high fidelityreverse transcriptase capable of carrying out reverse transcription withan error frequency of 2.0×10⁻⁵ or less at a temperature from about 45°to about 65° C. In further embodiments, the stabilized reversetranscriptase fusion protein is capable of carrying out substantiallevels of reverse transcription at temperatures up to about 81° C.

Another aspect of the invention provides a method for preparing a cDNAfrom an RNA molecule that includes the steps of: (a) adding a primernucleotide sequence to an RNA molecule and (b) incubating the RNAmolecule in the presence of one or more modified or unmodified deoxy ordideoxyribonucleoside triphosphates and a stabilized reversetranscriptase fusion protein that includes a thermostable reversetranscriptase connected to a stabilizer protein under conditionssufficient to synthesize a cDNA molecule complementary to all or aportion of the RNA molecule. In particular embodiments, the thermostablereverse transcriptase is connected to the stabilizer protein by a linkerpeptide (e.g., a non-cleavable or rigid non-cleavable linker peptide).Preferably, the reverse transcription is performed within a temperaturerange where RNA includes a substantially decreased amount of obstructingstable secondary or tertiary structure. Embodiments of this methodinclude ones in which the thermostable reverse transcriptase is a groupII intron-derived reverse transcriptase. In further embodiments of themethod, the thermostable reverse transcriptase includes a polypeptidewith an amino acid sequence identity that is substantially similar to asequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO: 3, SEQ ID NO: 4, or SEQ ID NO: 5, a non-cleavable linkerconsists of 1 to 20 amino acids, and the stabilizer protein is anaffinity protein or a solubility-enhancing protein. In yet furtherembodiments of the method, the reverse transcription is performed withan error frequency of 2.0×10⁻⁵ or less at a temperature from about 450to about 65° C.

Another aspect of the invention provides a DNA expression vector forproducing a stabilized reverse transcriptase fusion protein thatincludes a nucleic acid that encodes a polypeptide with an amino acidsequence identity that is substantially similar to a sequence selectedfrom the group consisting of SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8,SEQ ID NO: 9, or SEQ ID NO: 10.

Another aspect of the invention provides a method of producing astabilized reverse transcriptase fusion protein that includes the stepsof: (a) culturing a host cell that includes a DNA expression vector forproducing a stabilized reverse transcriptase fusion protein thatincludes a nucleic acid that encodes a polypeptide with an amino acidsequence identity that is substantially similar to a sequence selectedfrom the group consisting of SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8,SEQ ID NO: 9, or SEQ ID NO: 10; (b) expressing the stabilized reversetranscriptase fusion protein encoded by the DNA expression vector, and(c) isolating the stabilized reverse transcriptase fusion protein fromthe host cell.

The stabilized reverse transcriptase fusion protein can facilitate cDNAsynthesis at higher temperature, and/or with higher processivity, and/orallow the use of longer, more stable, primers that increase thespecificity (i.e., fidelity) of reverse transcription. The stabilized RTfusion protein of the invention can therefore be useful for a number ofapplications, such as research applications.

It is to be understood that both the foregoing general description andthe following detailed description are exemplary and explanatory onlyand are not restrictive of the invention, as claimed.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a listing of the amino acid sequence of a reversetranscriptase from Thermosynechococcus elongatus bound to a maltosebinding protein by a rigid linker (SEQ ID NO: 6). Amino acid residues1-367 represent the modified maltose binding protein (SEQ ID NO: 11):amino acid residues 368-372 represent the rigid linker (SEQ ID NO: 12);and amino acid residues 373-935 represent the TeI4c ORF (SEQ ID NO: 1).

FIG. 2 is a listing of the amino acid sequence of a reversetranscriptase from Thermosynechococcus elongatus bound to a maltosebinding protein by a rigid linker (SEQ ID NO: 7). Amino acid residues1-367 represent the maltose binding protein (SEQ ID NO: 11): amino acidresidues 368-372 represent the rigid linker (SEQ ID NO: 12); and aminoacid residues 373-935 represent the TeI4f ORF (SEQ ID NO: 2).

FIG. 3 is a listing of the amino acid sequence of a reversetranscriptase from Thermosynechococcus elongatus bound to a maltosebinding protein by a rigid linker (SEQ ID NO: 8). Amino acid residues1-367 represent the maltose binding protein (SEQ ID NO: 11); amino acidresidues 368-372 represent the rigid linker (SEQ ID NO: 12); and aminoacid residues 373-935 represent the TeI4h* ORF (SEQ ID NO: 3).

FIG. 4 is a listing of the amino acid sequence of a reversetranscriptase from Geobacillus stearothermophilus bound to a maltosebinding protein by a rigid linker (SEQ ID NO: 9). Amino acid residues1-367 represent the maltose binding protein (SEQ ID NO: 11); amino acidresidues 368-372 represent the rigid linker (SEQ ID NO: 12); and aminoacid residues 373-1008 represent the Geobacillus stearothermophilus GsI1ORF (SEQ ID NO: 4).

FIG. 5 is a listing of the amino acid sequence of a reversetranscriptase from Geobacillus stearothermophilus bound to a maltosebinding protein by a rigid linker (SEQ ID NO: 10). Amino acid residues1-367 represent the maltose binding protein (SEQ ID NO: 11); amino acidresidues 368-372 represent the rigid linker (SEQ ID NO: 12); and aminoacid residues 373-792 represent the Geobacillus stearothermophilus GsI2ORF (SEQ ID NO: 5).

FIG. 6 is a listing of the nucleotide sequence of the MalE-TeI4c openreading frame (ORF) rigid fusion of reverse transcriptase fromThermosynechococcus elongatus in the pMAL expression construct (SEQ IDNO: 13).

FIG. 7 is a listing of the nucleotide sequence of the MalE-TeI4f ORFrigid fusion of a reverse transcriptase from Thermosynechococcuselongatus in the pMAL expression construct (SEQ ID NO: 14).

FIG. 8 is a listing of the nucleotide sequence of the MalE-TeI4h* ORFrigid fusion of a reverse transcriptase from Thermosynechococcuselongatus in the pMAL expression construct (SEQ ID NO: 15).

FIG. 9 is a listing of the nucleotide sequence of the MalE-GsI1 ORFrigid fusion of a reverse transcriptase from Geobacillusstearothermophilus in the pMAL expression construct (SEQ ID NO: 16).

FIG. 10 is a listing of the nucleotide sequence of the MalE-GsI2 ORFrigid fusion of a reverse transcriptase from Geobacillusstearothermophilus in the pMAL expression construct (SEQ ID NO: 17).

FIG. 11 provides a graph showing the poly(rA)/oligo(dT)₄₂ assay ofreverse transcriptase (RT) activity at different temperatures. Theenzymes assayed were MalE-RF-GsI1, MalE-RF-GsI2, MalE-RF-TeI4c,MalE-RF-TeI4f, MalE-RF-TeI4h*, LtrA, and MalE-RF-LtrA. Reactions weredone by incubating the RT (50 nM for TeI4c and 100 nM for all other RTs)with 100 nM poly(rA)/oligo(dT)₄₂ and 5 μl [α-³²p]-dITP (3,000 Ci/mmol)in 75 mM KCl, 10 mM MgCl₂, 20 mM Tris-HCl, pH 7.5, and 1 mM DTI. Afterpreincubating the RT with poly(rA)/oligo(dT)₄₂ in the reaction mediumfor 1 min at the indicated temperature, the reaction was initiated byadding [α-³²P]-dTTP, incubated for times verified to be within thelinear range (90 sec for TeI4c RT and 5 min for all other RTs), andstopped by adding EDTA to a final concentration of 250 mM. Thepolymerization of [α-³²P]-dTTP into high-molecular weight material wasquantified by spotting the reaction products onto Whatman DE81chromatography paper (GE Health care Biosciences Corp), washing with 0.3M NaCl and 0.03 M sodium citrate, and scanning with a PhosphorImager toquantify radioactivity bound to the filter, as described in Materialsand Methods. The plot shows radioactivity bound to the filter(PhosphorImager units) as a function of reaction temperature.

FIG. 12 shows schematic representations of Group II intron RTs andfusion proteins. Section 12(A) provides comparison of group IIintron-encoded and retroviral RTs. Group II intron RTs exemplified bythe LtrA protein encoded by the Ll.LtrB intron generally contains fourmajor domains: RT, with conserved sequence blocks RT-1-7; X/thumb; DNAbinding (D), and DNA endonuclease (En). The RT and thumb domains ofgroup II intron RTs are homologous to those of retroviral RTsexemplified by HIV-1 RT, but are larger due to an N-terminal extensionand insertions upstream (RT-0) and between the conserved RT sequenceblocks (e.g., RT-2a, 3a, 4a, and 7a and thumb domain insertion ti inLtrA; Blocker et al., RNA 11, 14-28, 2005). The positions of threeα-helices characteristic of the thumb domains of retroviral RTs areshown for both LtrA and HIV-RT. The group II intron RTs used in thiswork all contain the En domain, except for the GsI2 RT, which lacks theEn domain. Section 12(B) shows group II intron RT fusion proteins. GroupII intron RTs (IEPs) were expressed with fused N-terminal MalE or NusAsolubility tags. Initial constructs contained the MalE solubility tag inexpression vector pMalE-c2t fused to the N-terminus of the RT via aflexible linker with a TEV protease cleavage site (underlined). Theseare shown as TVDEALKDAQTNS₃N₁₀LENLYFQGEF (SEQ ID NO: 19) andTVDEALKDAQTNS₃N₁₀L (SEQ ID NO: 44). A variant of these initialconstructs tested in FIG. 11 contained the pMalE-c2t linker with the TEVprotease cleavage site deleted. Improved constructs used modified MalEor NusA tags fused to the N-terminus of the RT via a rigid linkercontaining 5 alanine residues (underlined). These are shown asTVDAALAAAQTAAAAA (SEQ ID NO: 20) and MAARNICWFGAAAAA (SEQ ID NO: 46) Themodified MalE tag has charged amino acid residues changed to alanines(italics), and the modified NusA tag is missing the two C-terminal aminoacid residues.

FIG. 13 provides graphs showing the RT activity of derivatives ofMalE-RF-TeI4c RT with different rigid fusion linker or solubility tagsequences. Panel 13(A) provides a bar graph showing RT activity at 60°C. Reaction with MalE-RF-TeI4c RT (left bar) or variants containingdifferent tag or linker sequences (right bars) were done as in FIG. 11using 50 nM protein and 100 nM poly(rA)/oligo(dT)₄₂ and incubating for90 sec. Values are the mean for three determinations with error barsindicating the standard deviation. Panel 13(B) provides a graph showingthe temperature profile of RT activity for NusA-RF-TeI4c RT. RT activitywas assayed as in FIG. 11 using 50 nM protein and 100 nMpoly(rA)/oligo(dT)₄₂ and incubating for 2 min at the indicatedtemperature. The y-axis shows radioactivity bound to the filter(PhosphorImager units) for each protein (panel A) or for NusA-RF-TeI4cRT as a function of reaction temperature (panel B).

FIG. 14 provides graphs and autoradiograms that provide a comparison ofcDNA synthesis by MalE-RF-TeI4c, MalE-RF-GsI2, and SuperScript III RTactivity at different temperatures. In panels (A-C), the substrate was a531-nt RNA transcribed from AflIII-digested pBS KS(+) with an annealed5′-labeled 37-nt primer, and in panels (D-F), the substrate was a 1.2-kbkanR RNA with an annealed 5′-labeled 44-nt DNA primer. Reactions weredone by incubating 100 nM of annealed template/primer with 200 nM enzymein 100 mM KCl, 20 mM Tris HCl pH 7.5, 10 mM MgCl₂ and 10 mM DTT forMalE-RF-TeI4c RT (panels A and D) and MalE-RF-GsI2 RT (panels B and E)and in the manufacturer's buffer for SuperScript III RT (panels C andF). Reactions were initiated by adding dNTPs to a final concentration of1.25 mM, incubated for 30 min at the indicated temperature, andterminated by adding 0.1% SDS/250 mM EDTA (final concentrations)followed by phenol-CIA extraction. The products were analyzed byelectrophoresis in a denaturing 6% polyacrylamide gel, which was driedand quantified with a PhosphorImager. In each panel, the top and bottomautoradiograms show portions of the gel containing the full-lengthproduct (arrow) and unextended or partially extended primer,respectively, and the bar graphs show the percentage of primer that wasextended to full-length cDNA based on PhosphorImager quantitation. “?”indicates unidentified bands not used in quantitation of full-lengthproduct. A 5′-labeled 10-bp ladder (Invitrogen™) was used as sizemarkers. Schematics of two template primer substrates are shown at thebottom of the figure.

FIG. 15 is a listing of the nucleotide sequence of the 1.2-kb kanR RNAtemplate (SEQ ID NO: 21).

FIG. 16 provides semi-log plots obtained from qRT-PCR to compare amountsof cDNA synthesis at different temperatures by MalE-RF-TeI4c RT andSuperScript III RT. cDNA was synthesized with MalE-RF-TeI4c RT orSuperScript III RT (SSIII RT) using the 1.2-kb kanR RNA with annealedprimer P078 (Tm=80° C.) and detected with primer/probe sets at nt188-257 and nt 562-634 (the data for detection with primer set nt188-257 are shown in the figure; the data obtained with the primer setnt 562-634 are shown in FIG. 17). The qPCR amplification curves show asemi-log plot of fluorescence (ARN) versus cycle number. For eachsample, duplicate wells were analyzed and are depicted in eachamplification plot. The cycle threshold (C_(T)) values (the cycle atwhich the fluorescence crosses the threshold 0.4) for each cDNAsynthesis reaction by MalE-RF-TeI4c or SuperScript III RT are indicatedbelow the curves. Lower C_(T) values indicate a larger number of cDNAssynthesized

FIG. 17 provides semi-log plots obtained from qRT-PCR to compareprocessivity of cDNA synthesis by MalE-RF-TeI4c RT and SuperScript IIIRT. cDNA was synthesized with MalE-RF-TeI4c or SuperScript III RT usingthe 1.2-kb kanR RNA with annealed primer P078 (Tm=80° C.) and detectedwith primer/probe sets at nt 188-257 and nt 562-634. cDNA samples wereobtained at 60° C. (A, B) and 65° C. (C, D). For each sample,triplicates were analyzed and are depicted in each amplification plot.Average copy numbers are derived from a standard curve of quantitatedand diluted pET9 plasmid. Detection of similar numbers of cDNA copieswith the two primer sets, as seen for MalE-RF-TeI4c RT, shows that mostcDNAs extend to near the end of the RNA template, indicative of highprocessivity. A lower number of cDNA copies detected with the primer setnear the 5′ end (nt 188-257) compared to the primer set closer to the 3′end (nt 562-634), as seen for SuperScript III RT, indicates that the RTfalls off or is in some other way impeded from reaching the 5′ end ofthe RNA template.

FIG. 18 is a listing of the amino acid sequence of the NusAsolubility-enhancing protein (SEQ ID NO: 38).

DETAILED DESCRIPTION OF THE INVENTION

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. The terminology used in thedescription of the invention herein is for describing particularembodiments only and is not intended to be limiting of the invention.All publications, patent applications, patents, and other referencesmentioned herein are incorporated by reference in their entirety.

DEFINITIONS

As used in the description of the invention and the appended claims, thesingular forms “a,” “an,” and “the” are intended to include the pluralforms as well, unless the context clearly indicates otherwise. Inaddition, the recitations of numerical ranges by endpoints include allnumbers subsumed within that range (e.g., 1 to 5 includes 1, 1.5, 2,2.75, 3, 3.80, 4, 5, etc.).

As used herein, “polypeptide” refers to a polymer of amino acids anddoes not imply a specific length of a polymer of amino acids. Thus, forexample, the terms peptide, oligopeptide, protein, antibody, and enzymeare included within the definition of polypeptide. This term alsoincludes polypeptides with post-expression modification, such asglycosylation (e.g., the addition of a saccharide), acetylation,phosphorylation, and the like.

An “isolated” polypeptide or polynucleotide, as used herein, means apolypeptide or polynucleotide that has been either removed from itsnatural environment, produced using recombinant techniques, orchemically or enzymatically synthesized. Preferably, a polypeptide orpolynucleotide of this invention is purified, i.e., essentially freefrom any other polypeptide or polynucleotide and associated cellularproducts or other impurities.

“Amino acid” is used herein to refer to a chemical compound with thegeneral formula: NH₂—CRH—COOH, where R, the side chain, is H or anorganic group. Where R is organic, R can vary and is either polar ornonpolar (i.e., hydrophobic). The following abbreviations are usedthroughout the application: A=Ala=Alanine, T=Thr=Threonine,V=Val=Valine, C=Cys=Cysteine. L=Leu=Leucine, Y=Tyr=Tyrosine,I=Ile=Isoleucine, N=Asn=Asparagine, P=Pro=Proline, Q=Gln=Glutamine,F=Phe=Phenylalanine, D=Asp=Aspartic Acid, W=Trp=Tryptophan,E=Glu=Glutamic Acid, M=Met=Methionine, K=Lys=Lysine, G=Gly=Glycine,R=Arg=Arginine, S=Ser=Serine, H=His=Histidine. Unless otherwiseindicated, the term “amino acid” as used herein also includes amino acidderivatives that nonetheless retain the general formula.

A nucleotide consists of a phosphate group linked by a phosphoester bondto a pentose (ribose in RNA, and deoxyribose in DNA) that is linked inturn to an organic base. The monomeric units of a nucleic acid arenucleotides. Naturally occurring DNA and RNA each contain four differentnucleotides: nucleotides having adenine, guanine, cytosine and thyminebases are found in naturally occurring DNA, and nucleotides havingadenine, guanine, cytosine and uracil bases found in naturally occurringRNA. The bases adenine, guanine, cytosine, thymine, and uracil often areabbreviated A, G, C, T and U, respectively.

Nucleotides include free mono-, di- and triphosphate forms (i.e., wherethe phosphate group has one, two or three phosphate moieties,respectively). Thus, nucleotides include ribonucleoside triphosphates(e.g., ATP, UTP, CTG and GTP) and deoxyribonucleoside triphosphates(e.g., dATP, dCTP, dITP, dGTP and dTTP), and derivatives thereof.Nucleotides also include dideoxyribonucleoside triphosphates (ddNTPs,including ddATP, ddCTP, ddGTP, ddITP and ddTTP), and derivativesthereof.

“Substantially similar” means that a given nucleic acid or amino acidsequence shares at least 85%, more preferably at least 90%, and evenmore preferably at least 95% identity with a reference sequence.Furthermore, only sequences describing or encoding proteins in whichonly conservative substitutions are made in the conserved regions aresubstantially similar overall. Preferable, substantially similarsequences also retain the distinctive activity of the polypeptide.Substitutions typically seen as conservative substitutions are thereplacements, one for another, among the aliphatic amino acids Ala, Val,Leu and Ile; interchange of the hydroxyl residues Ser and Thr, exchangeof the acidic residues Asp and Glu, substitution between the amideresidues Asn and Gin, exchange of the basic residues Lys and Arg andreplacements among the aromatic residues Phe, Tyr.

A “promoter,” as used herein, refers to a sequence in DNA that mediatesthe initiation of transcription by an RNA polymerase. Transcriptionalpromoters may comprise one or more of a number of different sequenceelements as follows: 1) sequence elements present at the site oftranscription initiation; 2) sequence elements present upstream of thetranscription initiation site and, 3) sequence elements downstream ofthe transcription initiation site. The individual sequence elementsfunction as sites on the DNA, where RNA polymerases and transcriptionfactors that facilitate positioning of RNA polymerases on the DNA bind.

As used herein, the term “polymerase chain reaction” (“PCR”) refers to amethod for increasing the concentration of a segment of a targetsequence in a mixture of genomic DNA without cloning or purification.See for example Bartlett et al., Methods Mol. Biol. 226:3-6 (2003),which provides an overview of PCR and its development. This process foramplifying the target sequence typically consists of introducing a largeexcess of two oligonucleotide primers to the DNA mixture containing thedesired target sequence, followed by a precise sequence of thermalcycling in the presence of a DNA polymerase. The two primers arecomplementary to their respective strands of the double stranded targetsequence. To effect amplification, the mixture is denatured and theprimers then annealed to their complementary sequences within the targetmolecule. Following annealing, the primers are extended with apolymerase so as to form a new pair of complementary strands. The stepsof denaturation, primer annealing and polymerase extension can berepeated many times to obtain a high concentration of an amplifiedsegment of the desired target sequence. Unless otherwise noted, PCR, asused herein, also includes variants of PCR such as allele-specific PCR,asymmetric PCR, hot-start PCR, ligation-mediated PCR, multiplex-PCR,reverse transcription PCR, or any of the other PCR variants known tothose skilled in the art.

As used in this specification, whether in a transitional phrase or inthe body of the claim, the terms “comprise(s)” and “comprising” are tobe interpreted as having an open-ended meaning. That is, the terms areto be interpreted synonymously with the phrases “having at least” or“including at least”. When used in the context of a process, the term“comprising” means that the process includes at least the recited steps,but may include additional steps. When used in the context of a compoundor composition, the term “comprising” means that the compound orcomposition includes at least the recited features or components, butmay also include additional features or components.

A “fusion protein,” as used herein, refers to a protein having at leasttwo heterologous polypeptides covalently linked in which one polypeptidecomes from one protein sequence or domain and the other polypeptidecomes from a second protein sequence or domain.

Stabilized Reverse Transcriptase Fusion Protein

The invention provides a stabilized reverse transcriptase fusion proteinthat includes a thermostable reverse transcriptase connected to astabilizer protein. In many embodiments, the thermostable reversetranscriptase is connected to the stabilizer protein via a linkerpeptide. However, the thermostable reverse transcriptase and thestabilizer protein can also be directly fused to one another. Thepolypeptides that comprise the fusion protein are preferably linkedN-terminus to C-terminus. However, the reverse transcriptase and thestabilizer protein can be connected together in either order. Forexample, the two peptide sequences can be connected from the C-terminusto N-terminus or N-terminus to the C-terminus. In some embodiments, alinker peptide is included between the connecting C-terminus andN-terminus of the reverse transcriptase and stabilizer protein.

Attaching a stabilizer protein to the thermostable reverse transcriptasecan provide one or more advantages. A stabilized reverse transcriptasefusion protein can have one or more of the following advantages: (a)increased stability at elevated temperatures; (b) higher processivity,(c) increased solubility, and/or (d) higher fidelity. In someembodiments, a reverse transcriptase of the invention may have aplurality of the properties listed above. For example, a stabilizedreverse transcriptase fusion protein may have increased thermostabilityand increased fidelity. The advantages may sometimes derive from oneanother. For example, by providing increased solubility, the stabilizedreverse transcriptase fusion protein can provide a product able toprovide increased fidelity of transcription as a result of solubilizinga previously insoluble high fidelity thermostable reverse transcriptase.The use of a stabilizer protein in the fusion protein can also provideother advantages such as increased protein expression and improvedprotein folding. Inclusion of a linker peptide between the stabilizerprotein and the thermostable reverse transcriptase can further enhancethese advantages.

The stabilized reverse transcriptase fusion protein includes athermostable reverse transcriptase and a stabilizer protein, asdescribed herein. The stabilized reverse transcriptase fusion proteincan also includes a linker peptide. For example, the stabilized reversetranscriptase fusion protein can have an amino acid sequence as setforth in SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, or SEQID NO: 10, shown in FIGS. 1-5, respectively. Alternately, the stabilizedreverse transcriptase fusion protein can have an amino acid sequencethat is substantially similar to one or more of the sequences as setforth in SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, or SEQID NO: 10. A stabilized reverse transcriptase fusion protein amino acidsequence that is “substantially similar” to the fusion proteins providedby sequences 6-10 will share at least 85% identity, more preferably 90%identity and even more preferably 95% identity, and will include onlyconservative amino acid substitutions in conserved regions.

Thermostable Reverse Transcriptases

The present invention provides a reverse transcriptase fusion proteinthat includes a thermostable reverse transcriptase. The term “reversetranscriptases” (i.e., RNA-directed DNA polymerases) refers to a groupof enzymes having reverse transcriptase activity (i.e., that catalyzesynthesis of DNA from an RNA template). In general, such enzymesinclude, but are not limited to, retroviral reverse transcriptase,retrotransposon reverse transcriptase, and bacterial reversetranscriptases such as group 11 intron-derived reverse transcriptase,and mutants, variants or derivatives thereof. Examples of bacterialreverse transcriptase include Lactococcus lactis reverse transcriptase,Thermosynechococcus elongatus reverse transcriptase, or Geobacillusstearothermophilus reverse transcriptase. Further bacterial reversetranscriptases are described by Simon et al., Nucleic Acids Research,36, p. 7219-29 (2008), and Kojima and Kanehisa, Molecular Biology andEvolution, 25, p. 1395-04 (2008) which describe many classes of reversetranscriptases (i.e., retrons, group II introns, anddiversity-generating retroelements among others). Reverse transcriptasehas been used primarily to transcribe RNA into cDNA, which can then becloned into a vector for further manipulation or used in variousamplification methods such as polymerase chain reaction, nucleic acidsequence-based amplification (NASBA), transcription mediatedamplification (TMA), self-sustained sequence replication (3SR), diverseprimer extension reactions, 5′RACE, detection of chemical modificationsor other techniques that require synthesis of DNA using an RNA template.

The term “thermostable” refers to the ability of an enzyme or protein(e.g., reverse transcriptase) to be resistant to inactivation by heat.Typically such enzymes are obtained from a thermophilic organism (i.e.,a thermophile) that has evolved to grow in a high temperatureenvironment. Thermophiles, as used herein, are organisms with an optimumgrowth temperature of 45° C. or more, and a typical maximum growthtemperature of 70° C. or more. In general, a thermostable enzyme is moreresistant to heat inactivation than a typical enzyme, such as one from amesophilic organism. Thus, the nucleic acid synthesis activity of athermostable reverse transcriptase may be decreased by heat treatment tosome extent, but not as much as would occur for a reverse transcriptasefrom a mesophilic organism. “Thermostable” also refers to an enzymewhich is active at temperatures greater than 38° C., preferably betweenabout 38-100° C., and more preferably between about 40-81° C. Aparticularly preferred temperature range is from about 45° C. to about65° C.

In some embodiments, a thermostable reverse transcriptase retains atleast 50% (e.g., at least 60%, at least 70%, at least 80%, at least 90%,or at least 95%) of its nucleic acid synthetic activity after beingheated in a nucleic acid synthesis mixture at 90° C. for 30 seconds. Incontrast, typical reverse transcriptases will not work at elevatedtemperatures, and lose most of their nucleic acid synthetic activityafter such heat treatment. Thermostable reverse transcriptases typicallyalso have a higher optimum nucleic acid polymerization temperature.

Some reverse transcriptases are thermostable and therefore remainsubstantially active at temperatures commonly used in PCR-based nucleicacid synthesis. This provides the advantage of being able to carry outboth reverse transcription and DNA amplification in a single reactionenvironment. Such temperatures vary depending upon reaction parameters,including pH, template and primer nucleotide composition, primer length,and salt concentration. Thermostable reverse transcriptases includeThermosynechococcus elongatus (Te) RT, Geobacillus stearothermophilus(Gs) RT, modified forms of these RTs, and engineered variants of Avianmyoblastosis virus (AMV) RT, Moloney murine leukemia virus (M-MLV) RT,and Human immunodeficiency virus (HIV) RT. A reverse transcriptaseobtained from an organism living in an elevated temperature environment(i.e., greater than 37° C.) can be expected to be stable at the livingtemperature of the organism, and to a reasonable degree above.

A class of reverse transcriptases that is particularly suitable for usein stabilized reverse transcriptase fusion proteins are group IIintron-derived reverse transcriptases. A wide variety of group IIintron-derived reverse transcriptases are known. See for example theZimmerly Lab Website for Mobile Group II Introns that describes 105 fulllength group II intron-derived reverse transcriptases. The use of thiswebsite is described by Dai et al., Nucleic Acids Research, 31, p.424-26 (2003).

In certain embodiments the thermostable reverse transcriptase is onethat was encoded by a group II intron. Group II intron RTs typicallyconsist of four conserved domains: RT, which contains seven conservedsequence blocks (RT1-7) characteristic of the fingers and palm regionsof retroviral RTs; X, a region required for RNA splicing activitycorresponding at least in part to the thumb domain of retroviral RTs; D,a DNA-binding domain involved in DNA target site recognition; and En, aDNA endonuclease domain that cleaves the DNA target site to generate theprimer for reverse transcription (FIG. 12A; Blocker et al., RNA 11,14-28, 2005). The En domain is missing in some group II intron RTs,which instead use nascent strands at DNA replication forks to primereverse transcription (Zhong et al., EMBO J. 22, 4555-4565, 2003). TheRT and X/thumb domains of group II intron RTs are larger than those ofretroviral RTs due to an N-terminal extension, an additional N-terminalconserved sequence block (RT-0), and insertions between the conservedsequence blocks in the RT and X/thumb domain, some of which are sharedwith non-LTR-retrotransposon RTs. It has been suggested that thelarger-sized RT and thumb domains of group II intron and related RTsenable tighter binding of template RNAs leading to higher processivityand fidelity during reverse transcription. Unlike retroviral RTs, groupII intron RTs lack an RNase H domain and typically have very lowDNA-dependent DNA polymerase activity (Smith et al., Genes andDevelopment 19, 2477-2487, 2005).

Group II introns encode a class of RNAs known for their self-splicingreaction. Under certain in vitro conditions, group II intron-encodedRNAs can excise themselves from precursor mRNAs and ligate togethertheir flanking exons, without the aid of a protein. The splicingreaction mechanism is similar to the splicing of nuclear pre-mRNAintrons. A number of group II introns also encode reverse transcriptase(RT) open reading frames (ORF) and are active mobile elements. The ORFis typically found in domain DIV of the group II intron encoded RNA. Thegroup II intron RT assists RNA splicing by stabilizing the catalyticallyactive RNA structure and then remains bound to the excised intron RNA ina ribonucleoprotein (RNP) that promotes intron mobility by a processtermed “retrohoming.” Retrohoming occurs by a mechanism in which theexcised intron RNA in the RNPs inserts directly into a DNA target siteand is reverse transcribed by the RT. During retrohoming, in which thegroup II intron facilitates targeting of the intron to appropriate DNAsequences, the group II intron RT must produce an accurate cDNA copy ofthe intron RNA, which is typically 2-2.5 kb long and folds into highlystable and compact secondary and tertiary structures. Thus, group IIintron RTs must have high processivity and fidelity in order to carryout their biological function. Group II intron-derived RTs also lackRNase H activity, which can be beneficial because RNase H specificallydegrades the RNA of RNA:DNA hybrids, which allows any RNA to be copiedonly once and can lead to reduced yields of full length cDNA.

Based on the group II intron-derived reverse transcriptases so farevaluated, these RTs typically exhibit relatively high fidelity and highprocessivity. The fidelity of reverse transcription refers to thereliability of nucleotide incorporation during reverse transcription ofRNA to DNA, with higher fidelity describing nucleotide copying with alow number of errors (e.g., misincorporations). Higher specificity canbe provided by using longer and more specific primers, which requiresthe ability to carry out reverse transcription at higher temperatures.For example, a group II intron reverse transcriptase can provide reversetranscription with an error frequency of 2.0×10⁻⁵ or less, wherein theerror frequency represents the proportion of nucleotide copying errorsthat occur relative to the number of nucleotide copying events thatoccur without error. Other examples of high fidelity transcriptioninclude error frequencies of 1×10⁻⁴, 7.5×10⁻⁵, 5×10⁻⁵, 2.5×10⁻⁵, 1×10⁵,and 5×10⁻⁶. For further description of the high fidelity of group 11intron-derived RTs, see Conlan et al., Nucleic Acids Research. 33, p.5262-70 (2005).

Examples of suitable group II-derived intron reverse transcriptasesinclude the reverse transcriptases set forth in SEQ ID NO: 1, SEQ ID NO:2. SEQ ID NO: 3. SEQ ID NO: 4, and SEQ ID NO: 5, which are obtained fromThermosynechococcus elongatus (TeI4c, f, and h*) and Geobacillusstearothermophilus (GsI1 and GsI2). These sequences are shown in FIGS.1-5. The invention also encompasses group II intron derived reversetranscriptases that are substantially similar to those set forth in SEQID NO: 1, SEQ ID NO: 2. SEQ ID NO: 3. SEQ ID NO: 4, and SEQ ID NO: 5. Areverse transcriptase that is “substantially similar” to the reversetranscriptases provided by sequences 1-5 will share at least 85%identity, more preferably 90% identity and even more preferably 95%identity, and will include only conservative amino acid substitutions inconserved regions. The thermostability of a number of group IIintron-derived RTs is shown in FIG. 11, which demonstrates thatstabilized reverse transcriptase fusion proteins including the reversetranscriptases as set forth in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3,SEQ ID NO: 4, and SEQ ID NO: 5 have higher thermostability thanmesophilic Ll.LtrB reverse transcriptase, whether or not it is part of afusion protein, when evaluated as shown in FIG. 11. The mesophilicLl.LtrB showed a temperature optimum of about 35° C. either alone or aspart of a fusion protein.

As noted herein, modified forms of thermostable group II intron-derivedRTs can also be used. For example, SEQ ID NO: 3, the TeI4h* RT, does notrepresent a native form of reverse transcriptase, but rather is aderivative in which the active site was modified from the amino acidsequence YAGD to the amino acid sequence YADD, to more closely resemblethe active site of other active group II intron-derived RTs.

The amount by which a given amino acid sequence is “substantiallysimilar” to a reference sequence can be determined for example, bycomparing sequence information using sequence analysis software such asthe Blastp program, version 2.2.10, of the BLAST 2 search algorithm, asdescribed by Tatusova et al. (FEMS Microbiology Letters, 174, p. 247-50(1999)), and available on the world wide web at the National Center forBiotechnology Information website, under BLAST in the Molecular Databasesection. Preferably, the default values for all BLAST 2 searchparameters are used, including matrix=BLOSUM62; open gap penalty=11,extension gap penalty=1, gap x_dropoff=50, expect=10, wordsize=3, andoptionally, filter on. In the comparison of two amino acid sequencesusing the BLAST search algorithm, structural similarity is referred toas “similarity” and identity is referred to as “identity.”

Amino acid identity is defined in the context of a comparison between acandidate polypeptides and a reference amino acid sequence, and isdetermined by aligning the residues of the two amino acid sequences(i.e., a candidate amino acid sequence and the reference amino acidsequence) to optimize the number of identical amino acids along thelengths of their sequences; gaps in either or both sequences arepermitted in making the alignment in order to optimize the number ofidentical amino acids, although the amino acids in each sequence mustnonetheless remain in their proper order.

Information is available to support a structure-function correlation forgroup II intron-derived reverse transcriptases. See for example Simon etal., Nucleic Acids Research, 36, p. 7219-29 (2008), which classifies andaligns the RT domains of bacterial reverse transcriptases, and Xiong etal., EMBO J., 9, p. 3353-62 (1990), which provides an alignment of 82 RTsequences showing seven conserved domains and 42 conserved positions.See also Blocker et al, RNA, 11, p. 14-28 (2005), which provides athree-dimensional model of Lactococcus lactis Ll.LtrB intron RT (theLtrA protein), describes the proteolytic cleavage sites and conservedregions, and provides a sequence alignment analysis of LtrA relative toHIV-1 RT. Accordingly, a variety of stabilized reverse transcriptasefusion proteins that are substantially similar to those set forth in SEQID NO. 6-10 can readily be obtained by modification of amino acidsoutside of the conserved regions, and only conservative modification ofamino acids within the known conserved regions.

In one embodiment, the present invention provides a stabilized reversetranscriptase fusion protein having a reverse transcriptase activitythat has a half-life of greater than that of the corresponding unboundreverse transcriptase at an elevated temperature, i.e., greater than 37°C. In some embodiments, the half-life of a reverse transcriptase of thepresent invention may be 5 minutes or greater and preferably 10 minutesor greater at 50° C. In some embodiments, the reverse transcriptases ofthe invention may have a half-life (e.g., at 50° C.) equal to or greaterthan about 25 minutes, preferably equal to or greater than about 50minutes, more preferably equal to or greater than about 100 minutes, andmost preferably, equal to or greater than about 200 minutes.

Stabilizer Proteins

The stabilized reverse transcriptase fusion protein of the presentinvention also includes a stabilizer protein. A stabilizer protein, asdefined herein, is a protein forming part of the fusion protein thatfunctions to increase the overall stability of the fusion protein.Stability includes the ability of the protein to retain its conformationand activity. In addition, the stabilizer protein preferably enhancesthe solubility of the fusion protein, as further described herein withregard to solubility-enhancing proteins. This can be particularlyhelpful with regard to group II intron RTs, which have been found to bepoorly expressed and insoluble in the absence of the intron RNA to whichthey are ordinarily tightly bound in RNPs. (Vellore et al. Appl.Environ. Microbiol. 70, 7140-7147, 2004; Ng et al., Gene 393, 137-144,2007) Effective stabilizer proteins include those that include anindependent folding domain and/or do not fold into long-lived misfoldedintermediates that can influence the propensity of proteins toaggregate. Proteins that will provide an independent folding domain aredescribed by Janin et al., Progress in Biophysics and Molecular Biology,42, p. 21-78 (1983), and proteins that do not fold into long-livedmisfolded intermediates are described by Idicula et al., ProteinScience, 14, p. 582-592 (2005). For example, the stabilizer protein canbe a protein that includes 50 or more amino acids. In other embodiments,the stabilizer protein can be a larger protein including 100 or moreamino acids. As exemplified by the maltose binding protein and NusAproteins provided herein, the stabilizer proteins can also have a sizefrom about 250 amino acids to about 400 amino acids. The stabilizerprotein can also be a thermostable protein.

The stabilizer protein can also be or include an affinity protein. Theterm affinity protein, as used herein, refers to a protein for whichthere is a readily available ligand that exhibits a high bindingconstant (i.e., “affinity”) for the protein. Affinity proteins are oftenused in the role of an affinity tag. Affinity proteins, as is known tothose skilled in the art, can be provided in fusion proteins tofacilitate the purification of the protein connected or fused to theaffinity protein by techniques such as affinity purification, in which atag binds to a ligand within an affinity column. Suitable affinityproteins are known in the art. See for example Waugh, D., Trends inBiotechnology, 23, p. 316-320 (2005), which describes a number ofsuitable affinity proteins, including glutathione S-transferase,maltose-binding protein, FLAG-tag peptide, biotin acceptor peptide,streptavidin-binding peptide, and calmodulin-binding peptide. For thepreparation and use of fusion proteins that include an affinity protein,see for example U.S. Pat. Nos. 5,643,758, 5,654,176, and 7,001,745.

The stabilizer protein can also be a solubility-enhancing protein.Recombinantly-expressed fusion proteins can exhibit low solubility intheir host cells and/or in subsequent method applications, which can beameliorated through inclusion of a solubility-enhancing protein in thefusion protein that substantially increases the solubility of the fusionprotein in aqueous environments. Some solubility-enhancing proteins usedare also affinity proteins, and can therefore be described assolubility-enhancing affinity proteins. Examples of solubility-enhancingproteins include sugar binding proteins such as arabinose bindingprotein, chitin binding protein, cellulose binding protein, and maltosebinding protein. Other examples of solubility-enhancing proteins includethe NusA and Dsb solubility tags provided by Novagen®, and thesolubility enhancing tag (SET) provided by Invitrogen™. Harrison hasdemonstrated the very high solubility provided by the NusA solubilitytag, while the solubility enhancement of Dsb is described byCollins-Racie. See Harrison, R. G., inNovations, 11, p. 4-7 (2000), andCollins-Racie et al., Biotechnology, 13, p. 982-87 (1995).

In some embodiments, stabilizer proteins such as solubility-enhancingproteins or affinity proteins can be modified to improve theirperformance. Modification can include providing one or moresubstitutions, additions or deletions of amino acids within the proteinsequence of the stabilizer protein as compared to the normal, wild-typesequence of the protein. For example, a stabilizer protein such as anaffinity protein or a solubility-enhancing protein can be modified byreplacing the charged amino acids with uncharged amino acids in certainregions of the protein. Charged amino acids include amino acids withpositively or negatively charged side chains. Examples of amino acidswith positively charged side chains include arginine, histidine, lysine,and the like. Examples of amino acids with negatively charged sidechains include aspartic acid and glutamic acid, and the like. Unchargedamino acids include, but are not limited to, alanine, serine, threonine,glutamine, valine, leucine, isoleucine, phenylalanine, and tyrosine. Forexample, a maltose binding protein can be modified by replacing one ormore of the charged amino acids with alanine.

Examples of suitable affinity proteins include the maltose bindingprotein amino acid sequence set forth in SEQ ID NO: 11, shown in FIGS.1-5, and sequences substantially similar to SEQ ID NO: 11. Note thatwhile modification of the affinity protein is not necessary, the maltosebinding protein set forth in SEQ ID NO: 11 was modified to replace threecharged amino acids with alanine near the C-terminus. Another suitableprotein, in this case a solubilizing protein, is the N-utilizationsubstance A (NusA) protein, which has the amino acid sequence set forthin SEQ ID NO: 38, shown in FIG. 18. In additional embodiments of theinvention, fusion proteins described herein that include the maltosebinding proteins can have the maltose binding protein replaced withN-utilization substance A proteins.

Linker Peptides

In some embodiments, the stabilized reverse transcriptase fusion proteinalso includes a linker peptide positioned between the stabilizer proteinand the thermostable reverse transcriptase. Preferably, the linkerpeptide is a non-cleavable linker peptide. By “positioned between,” itis meant that the linker peptide is connected by a chemical linkage(e.g., an amide linkage) to the N or C terminal of each of thestabilizer protein and the reverse transcriptase, as described in regardto fusion proteins herein. For example, the linker peptide can beconnected through an amide linkage to the C terminal region of thestabilizer protein and the N terminal region of the thermostable reversetranscriptase. By non-cleavable, it is meant that the linker peptide isnot readily susceptible to cleavage by a protease.

In additional embodiments, the linker peptide is a rigid linker peptide;i.e., a relatively non-flexible peptide linker. Rigid linker peptidesare not required to completely lack flexibility, but rather aresignificantly less flexible than flexible linker peptides such asglycine-rich peptide linkers. Rigid linker peptides, as a result oftheir relative lack of flexibility, decrease the movement of the twoprotein domains attached together by the rigid linker peptide, which inthe present case are the stabilizer protein and the thermostable reversetranscriptase. Linker peptides that provide ordered chains such as alphahelical structure can provide rigid linker peptides. For example,Arginine, Leucine, Glutamate, Glutamine, and Methionine all show arelatively high propensity for helical linker formation. However, anon-helical linker including many proline residues can exhibitsignificant rigidity as well. Examples of rigid linkers includepolylysine and poly-DL-alaninepolylysine. Further description of rigidpeptide linkers is provided by Wriggers et al., Biopolymers, 80, p.736-46 (2005). In addition, rigid linker peptides are described at thelinker database described by George et al., Protein Engineering, 15, p.871-79 (2003). Preferably, the rigid linker peptide is also anon-cleavable linker peptide; i.e., a non-cleavable, rigid linkerpeptide.

Relatively short polypeptides are preferred for use as linker peptides.For example, linker peptides can include from 1 to 20 amino acids.Linker peptides can also include from 1 to 15, from 1 to 10, from 1 to5, or from 3 to 5 amino acids. Examples of specific sequences that canbe used as linker peptides include dipeptides, tripeptides,tetrapeptides, and pentapeptides formed of alanine amino acids. Onesuitable rigid linker peptide is AAAAA (SEQ ID NO: 12), while anothersuitable rigid linker peptide is AAAEF (SEQ ID NO: 18). Use of a linkerpeptide (e.g., a rigid linker peptide) in a fusion protein can provideone or more advantages. For example, while not intending to be bound bytheory, it is believed that use of a rigid linker peptide can stabilizethe fusion protein by decreasing the amount of movement of the twohalves of the fusion protein relative to one another. While very short(i.e., 1 or 2 amino acid) linkers can be used, it is preferable to uselinkers that include from 3 to 5 amino acids.

The linker peptide can be either cleavable or non-cleavable by aprotease. Affinity proteins are often associated to another protein in afusion protein using a cleavable peptide so that the affinity proteincan be removed. However, in the present invention the stabilizer protein(e.g., an affinity protein) remains bound to the reverse transcriptase,for the reasons described herein. Accordingly, it is generallypreferable that the linker peptide be non-cleavable. However, cleavablelinkers can be used in some embodiments. For example, cleavable linkers,including rigid cleavable linker peptides, that are susceptible toprotease cleavage can be used if it is desirable to remove thestabilizer protein during a subsequent step and exposure to the cleavingprotease is avoided during use of the fusion protein.

Use of Stabilized Reverse Transcriptase Fusion Proteins

The invention also provides a method for preparing a cDNA from an RNA(e.g., mRNA, rRNA, tRNA, and miRNA), which is required for other methodssuch as the reverse transcription polymerase chain reaction (RT-PCR). Asused herein, the term “RT-PCR” refers to the replication andamplification of RNA sequences. In this method, reverse transcription iscoupled to PCR, e.g., as described in U.S. Pat. No. 5,322,770. InRT-PCR, the RNA template is converted to cDNA due to the reversetranscriptase activity of an enzyme, and then amplified using thepolymerizing activity of the same or a different enzyme.

In the practice of the invention, cDNA molecules may be produced bymixing one or more nucleic acid molecules (e.g., RNA) obtained fromcells, tissues, or organs using methods that are well known in the art,with the composition of the invention, under conditions favoring thereverse transcription of the nucleic acid molecule by the action of theenzymes of the compositions to form a cDNA molecule (single-stranded ordouble-stranded). Thus, the method of the invention comprises (a) mixingone or more nucleic acid templates (preferably one or more RNA or mRNAtemplates, such as a population of mRNA molecules) with stabilized RTfusion protein of the invention and (b) incubating the mixture underconditions sufficient to permit cDNA synthesis of all or a portion ofthe one or more nucleic acid templates.

In one aspect, the method includes the steps of (a) adding a primer toan RNA molecule and (b) incubating the RNA molecule in the presence ofone or more deoxy or dideoxyribonucleoside triphosphates and astabilized reverse transcriptase fusion protein comprising athermostable reverse transcriptase connected to a stabilizer proteinunder conditions sufficient to synthesize a cDNA molecule complementaryto all or a portion of the RNA molecule. Adding the primer to an RNAmolecule may include hybridizing the primer to the RNA molecule. In someembodiments, the stabilized reverse transcriptase fusion protein canalso include a linker peptide connecting the stabilizer protein to thethermostable reverse transcriptase. Preferably, the reversetranscription is performed within a temperature range where the RNAincludes a substantially decreased amount of obstructing stablesecondary or tertiary structure. This can be a temperature from about45° C. to about 81° C., with a more preferred temperature range beingfrom about 45° C. to about 65° C. This can also be described as atemperature range in which the RNA does not form a significant amount ofstable secondary or tertiary structure. Due to the high fidelity andother advantages of group II intron-derived RTs, their use may bepreferred. For example, the stabilized reverse transcriptase fusionprotein can include a group II intron-derived reverse transcriptase withan amino acid sequence identity that is substantially similar to asequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO: 3, SEQ ID NO: 4, or SEQ ID NO: 5, a non-cleavable linkerconsisting of 1 to 20 amino acids, and the stabilizer protein comprisesa solubility-enhancing or affinity protein. The stabilized reversetranscriptase fusion protein can also include a linker peptide betweenthe stabilizer peptide and the reverse transcriptase, which can have alength from 1-20 amino acids, can be a non-cleavable linker, or can berigid linker. Embodiments of the method can perform reversetranscription with an error frequency of 2.0×10⁻⁵ or less. Particularlyat a temperature from about 45° C. to about 65° C.

The stabilized reverse transcriptase fusion proteins can also be used inother applications. For example, stabilized RT fusion proteins can beused for the cloning of differentially expressed 5′ ends of mRNAs; aprocess referred to as rapid amplification of cDNA ends (RACE) andvariations thereof such as RNA ligase mediated RACE (RLM-RACE).Stabilized RT fusion proteins can also be used for the mapping ofchemical footprints in RNA, differential display RT-PCR, which allowsfor the analysis of gene expression among cell populations, and in-situPCR for medical diagnosis.

Preparation of Stabilized Reverse Transcriptase Fusion Proteins

An expression vector containing a stabilized reverse transcriptasefusion protein-encoding nucleic acid molecule may be used for high-levelexpression of stabilized reverse transcriptase fusion protein in arecombinant host cell. Expression vectors may include, but are notlimited to, cloning vectors, modified cloning vectors, specificallydesigned plasmids or viruses. A variety of expression vectors may beused to express recombinant stabilized reverse transcriptase fusionsequences in appropriate cell types. For example, bacterial vectors,mammalian vectors, fungal vectors, and insect vectors may be used forexpression in bacteria, mammalian cells, fungal cells, and insect cells,respectively.

Stabilized reverse transcriptase fusion proteins can be prepared byobtaining a nucleotide sequence capable of expressing a stabilizedreverse transcriptase fusion protein and then expressing that nucleotidesequence in a host cell. The stabilized reverse transcriptase fusionproteins expressed by the host cell can then be purified using a varietyof techniques known to those skilled in the art, depending in part onthe nature of the host cell.

Nucleotide sequences capable of expressing stabilized reversetranscriptase fusion proteins of the invention can be prepared using avariety of methods known to those skilled in the art. For example, thenucleotide sequences can be prepared using recombinant plasmids in whichvarious linkers, reverse transcriptases, and stabilizer proteins arecombined, as described in Example 1 herein.

The present invention also relates to host cells transformed ortransfected with vectors comprising a nucleic acid molecule capable ofexpressing a stabilized reverse transcriptase fusion protein.Recombinant host cells may be prokaryotic or eukaryotic, including butnot limited to, bacteria such as E. coli, fungal cells such as yeast,mammalian cells including, but not limited to, cell lines of bovine,porcine, monkey and rodent origin; and insect cells including but notlimited to Drosophila and silkworm derived cell lines. Such recombinanthost cells can be cultured under suitable conditions to produce astabilized reverse transcriptase fusion protein or a biologicallyequivalent form. As defined herein, the term “host cell” is not intendedto include a host cell in the body of a transgenic human being, humanfetus, or human embryo.

As noted above, an expression vector containing DNA encoding astabilized reverse transcriptase fusion protein may be used forexpression of stabilized reverse transcriptase fusion protein in arecombinant host cell. Therefore, another aspect of this invention is aprocess for expressing a stabilized reverse transcriptase fusion proteinin a recombinant host cell, comprising: (a) introducing a vectorcomprising a nucleic acid comprising a sequence of nucleotides thatencodes a stabilized reverse transcriptase fusion protein into asuitable host cell, wherein the stabilized reverse transcriptase fusionprotein comprises a thermostable reverse transcriptase connected to astabilizer protein directly or via a linker and (b) culturing the hostcell under conditions which allow expression of the stabilized reversetranscriptase fusion protein. The stabilized reverse transcriptionfusion protein can be varied to include any of the features describedherein, such as the inclusion of a linker peptide connecting thethermostable reverse transcriptase and the stabilizer protein.

Following expression of a stabilized reverse transcriptase fusionprotein in a host cell, the stabilized reverse transcriptase fusionprotein may be recovered to provide purified stable reversetranscriptase fusion protein. Several protein purification proceduresare available and suitable for use. For instance, see Example 2 providedherein. Recombinant protein may be purified from cell lysates andextracts by various combinations of, or individual application of saltfractionation, ion exchange chromatography, size exclusionchromatography, hydroxylapatite adsorption chromatography andhydrophobic interaction chromatography. The use of affinity tags in someembodiments of the invention can facilitate purification of the protein.For example, the stabilized reverse transcriptase fusion protein can beseparated from other cellular proteins by use of an immunoaffinitycolumn made with monoclonal or polyclonal antibodies specific for thereverse transcriptase or stabilizer protein portion of the fusionprotein. Heating can be used to separate the stabilized reversetranscriptase fusion protein from host proteins, which are not stable atelevated temperatures and will therefore precipitate.

The nucleic acids capable of expressing a stabilized RT fusion proteinmay be assembled into an expression cassette which comprises sequencesdesigned to provide for efficient expression of the fusion protein in ahost cell. The cassette preferably contains a stabilized reversetranscriptase fusion protein-encoding open reading frame, with relatedtranscriptional and translations control sequences operatively linked toit, such as a promoter, and termination sequences. For example, the openreading frame can include a nucleic acid that encodes a polypeptide withan amino acid sequence identity that is substantially similar to asequence selected from the group consisting of SEQ ID NO: 6, SEQ ID NO:7, SEQ ID NO: 8, SEQ ID NO: 9, or SEQ ID NO: 10, as shown in FIGS. 1-5,respectively. In a preferred embodiment, the promoter is a T7 or a tacpromoter for expression in E. coli, although those skilled in the artwill recognize that any of a number of other known promoters may beused. E. coli also has rho independent and dependent terminators and canuse T7 polymerase for rapid DNA replication. In eukaryotic cells,inclusion of a polyadenylation site will be helpful for the correctprocessing of mRNA.

The open reading frame can also include polynucleotide sequences as setforth in SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15. SEQ ID NO: 16, andSEQ ID NO: 17, as shown in FIGS. 6-10, respectively. Alternately, theopen reading frame can include polynucleotide sequences that aresubstantially similar to those set forth in SEQ ID NO: 13, SEQ ID NO:14. SEQ ID NO: 15, SEQ ID NO: 16, and SEQ ID NO: 17. In this particularcontext, the term “substantially similar” refers to variants in thenucleotide sequence in which codons that encode the same amino acid canbe used interchangeably such that the nucleotide sequence will stillresult in the translation of an amino acid sequence corresponding to SEQID NO: 6-10. The stabilized reverse transcriptase fusion protein openreading frame polynucleotide preferably has at least about 80% identity,at least about 90% identity, at least about 95% identity, or at leastabout 98% identity to a polynucleotide sequence selected from the groupconsisting of SEQ ID NO: 13. SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO:16, and SEQ ID NO: 17.

Nucleotide identity is defined in the context of a comparison between acandidate stabilized reverse transcriptase fusion protein open readingframe and a polynucleotide sequence selected from the group consistingof SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, and SEQID NO: 17, and is determined by aligning the residues of the twopolynucleotides to optimize the number of identical nucleotides alongthe lengths of their sequences; gaps in either or both sequences arepermitted in making the alignment in order to optimize the number ofshared nucleotides, although the nucleotides in each sequence mustnonetheless remain in their proper order. Preferably, two nucleotidesequences are compared using the Blastn program of the BLAST 2 searchalgorithm, as described by Tatusova, et al. (FEMS Microbiology Letters,174, p. 247-50 (1999)), and available on the world wide web at theNational Center for Biotechnology Information website, under BLAST inthe Molecular Database section. Preferably, the default values for allBLAST 2 search parameters are used, including reward for match=1,penalty for mismatch=−2, open gap penalty=5, extension gap penalty=2,gap×dropoff=50, expect=10, wordsize=11, and optionally, filter on. Inthe comparison of two nucleotide sequences using the BLAST searchalgorithm, nucleotide identity is referred to as “identities.”

With regard to protein preparation from nucleotide sequences, it isnoted that a “triplet” codon of four possible nucleotide bases can existin over 60 variant forms. Because these codons provide the message foronly 20 different amino acids (as well as transcription initiation andtermination), some amino acids can be coded for by more than one codon,a phenomenon known as codon redundancy. Accordingly, the nucleotidesequences used to prepare the particular amino acid sequences ofstabilized reverse transcriptase fusion proteins can vary considerably,depending on the particular codons used. For reasons not completelyunderstood, alternative codons are not uniformly present in theendogenous DNA of differing types of cells, and there exists a naturalhierarchy or “preference” for certain codons in certain types of cells.Accordingly, in some embodiments the choice of codons used to express astabilized reverse transcriptase fusion protein may be optimized throughuse of particular codons to result in higher levels of expression.

In accordance with this invention, the stabilized reverse transcriptasefusion protein expression cassette is inserted into a vector. The vectoris preferably a plasmid or adenoviral vector, although linear DNA linkedto a promoter, or other vectors, such as adeno-associated virus or amodified vaccinia virus, retroviral or lentiviral vector may also beused. In particular, the use of E. coli plasmid vectors is preferred.

A detailed description of the work conducted by the inventors to developand evaluate stabilized reverse transcriptase fusion proteins isprovided below.

Expression and Purification of Group H Intron RTs as MalE FusionProteins

The expression and solubility of poorly behaved proteins can sometimesbe improved by fusion of highly soluble proteins, like maltose-bindingprotein (MalE) or N utilization substance A (NusA) (Nallamsetty et al.,Protein Expression and Purification 45, 175-182, 2005). The MalE tagadditionally permits facile purification of the protein viaamylose-affinity chromatography. The inventors therefore tested whethergroup II intron RTs could be expressed and purified as MalE fusions.Initially, a MalE tag was fused to the N-terminus of the RT via a TEVprotease-cleavable linker in the expression vector pMal-c2t (FIG. 12B).The MalE-RT fusion proteins for several of the T. elongatus group IIintron RTs expressed well in E. coli and could be purified by aprocedure that involves polyethyleneimine (PEI)-precipitation to removenucleic acids, followed by amylose-affinity and heparin-Sepharosechromatography. Further, the uncleaved MalE-RT fusion proteins assayedsoon after purification had high thermostable RT activity. However, theyields of these proteins were <0.2 mg/l for the Thermosynechococcusproteins. Additionally, when the MalE tag was removed by cleavage withTEV protease, the RTs immediately formed an insoluble precipitate, whileif the tag was left uncleaved, the MalE-RT fusion proteins progressivelylost RT activity and were degraded within days, even when stored on iceor flash frozen in 50% glycerol. The latter findings were surprisingbecause proteins that fold properly in the presence of a solubility tagtend to remain soluble after cleavage of the tag (Nallamsetty et al.,Protein Expression and Purification 45, 175-182, 2005). The group IIintron RTs, which were active with but not without the attached MalEtag, appear to be an exception. The finding that the stabilizer proteinmust remain attached to the thermostable reverse transcriptase suggeststhat it plays an active role in keeping the thermostable reversetranscriptase soluble and active.

To overcome these difficulties, the inventors tested whether the groupII intron RTs could be stabilized in active form by attaching the MalEtag to the protein via a non-cleavable rigid linker. Such MalE-rigidfusions typically have a linker region of 3 to 5 alanine residuescombined with changes at the C-terminus of the MalE tag to replacecharged amino acid residues with alanines (Smyth et al., Genes andDevelopment 19, 2477-2487, 2003). These rigid fusion linkers reduceconformational heterogeneity, enabling crystallization of proteins withattached linkers for structure determination (Smyth et al., ibid). Forthe MalE-RF-RT fusions tested here, the MalE/linker region of pMal-c2tTVDEALKDAQTNS₃N₁₀LENLYFQGEF (SEQ ID NO: 19) was modified toTVDAALAAAQTAAAAA (SEQ ID NO: 20) and called a MalE-RF (rigid fusion) tag(FIG. 12B).

To rapidly assess whether the MalE-RF tag affects the activity of groupH intron RTs, the inventors tested whether the MalE-RF-RTs could supportretrohoming in vivo. For initial tests, the RTs chosen were the LtrAprotein encoded by the L. lactis Ll.LtrB intron, and TeI4h* RT, anactivated derivative of the RT encoded by the thermostable T. elongatusTeI4h intron. In retrohoming assays at 37° C., the MalE-RF-LtrA proteinsupported retrohoming at an efficiency of 20% compared to 86% for nativeLtrA, while in retrohoming assays at 48° C., the MalE-RF-TeI4h* proteinsupported retrohoming at an efficiency of 87% compared to 100% for theunfused TeI4h* protein; see Table 1. Thus remarkably both MalE-RF-RTsretain the ability to support retrohoming with high albeit somewhatreduced efficiencies despite the presence of the attachedmaltose-binding protein rigid linker sequence. These findings imply thatthe proteins retain substantial levels of all activities required forretrohoming, including RT, RNA splicing, and DNA endonuclease activity.This mobility assay provides a convenient screen for active group IIintron RTs.

TABLE 1 Retrohoming efficiencies for different RTs RT Efficiency TeI4h*(48° C.) 100% MalE-RF-TeI4h* (48° C.) 87% LtrA (37° C.) 86% MalE-RF-LtrA(37° C.) 20%

Retrohoming assays were done in E. coli HMS174(DE3) as describedpreviously for the Ll.LtrB intron (LtrA protein) (Guo et al. Science289, 452-457, 2000, Karberg et al. Nature Biotech. 19, 1162-1167, 2001)and TeI4h*. The Cap^(R) intron-donor plasmids use a T7lac promoter toexpress a ΔORF intron (I-ΔORF) with short flanking 5′ and 3′ exons (E1and E2, respectively) and a T7 promoter in DIV, followed by the RT ORFdownstream of E2. The Amp^(R) recipient plasmids contain a target sitefor the intron (ligated E1-E2 sequences) cloned upstream of apromoterless tet^(R) gene. Intron expression was induced with IPTG (0.1mM for LtrA and MalE-RF-LtrA and 0.5 mM for TeI4h* and MalE-RF-TeI4h*)for 1 h at the indicated temperature. Retrohoming of the intron carryingthe T7 promoter into the target site activates the expression of thetet^(R) gene, enabling selection for Tet^(R)+Amp^(R) colonies.Retrohoming efficiencies were calculated as the ratio of(Amp^(R)+Tet^(R))/Amp^(R) colonies.

Encouraged by these findings, the inventors constructed plasmids inwhich several group II intron RTs were expressed with a MalE tag fusedto the N-terminus of the protein via a rigid linker in the vectorpMal-c2t. The RTs tested included several T. elongatus group II intronRTs, whose ability to support retrohoming had been tested previouslyusing the above plasmid assay and two G. stearothermophilus group IIintron RTs related to group II intron RTs that had previously beendifficult to purify with high yield and activity (Vellore et al., Appl.Environ. Microbiol. 70, 7140-7147, 2004; Ng et al., Gene 393, 137-144,2007). In some constructs, the inventors added an additional C-terminalHis6-tag to enrich for full-length protein in the purification. TheMalE-RF-RT fusion proteins were expressed in E. coli and purified by aprocedure that involves PEI-precipitation of nucleic acids followed byamylose-affinity and heparin-Sepharose chromatography. An additional Nicolumn chromatography step was included for constructs with a C-terminalHis6 tag. The proteins were dialyzed against the purification bufferwith 50% glycerol, flash frozen, and stored at −80° C. The final proteinpreparations were >95% pure with yields of 0.5-2.2 mg/ml and their RTactivity was undiminished after storage for at least six months.

RT Assays

To assess their thermostability, the inventors first assayed the RTactivity of fusions MalE-RF-TeI4c, TeI4h*, and TeI4f fromThermosynechococcus elongatus and MalE-RF-GsI1 and GsI2 from Geobacillusstearothermophilus at temperatures between 25 and 77° C. These initialassays were done by using poly(rA)/oligo(dT)₄₂ as the template-primersubstrate and quantifying polymerization of ³²P-dTTP into high molecularweight material. The relatively long 42-nt dT primer was used so that itwould remain annealed to the poly(rA) template at higher temperatures(calculated Tm=69° C.). The LtrA protein with and without an N-terminalMalE-RF tag was assayed in parallel as a mesophilic RT control (FIG.11). Whereas the LtrA protein had a temperature optimum of ˜35° C. withor without the MalE rigid fusion tag, the other five MalE-RF-RT's hadhigher temperature optima ranging from 45-61° C. The two most active andthermostable RTs, MalE-RF-GsI2 and MalE-RF-TeI4c had temperature optimaof 61° C. and retained substantial activity at 70° C. (where the assaymay be limited by the stability of the primer-template base pairing). Ofthe two RTs, MalE-RF-TeI4c had the highest activity and was assayed atlower protein concentrations (50 nM) and for shorter times (90 sec) thanthe other RTs (100 nM, 5 min) in order to remain within the linearrange. Tests with the MalE-RF-TeI4c protein showed that inclusion ofmaltose (10 μM to 1 mM), which can affect the conformation of the MalEtag, had little if any effect on RT activity.

Effect of Changing the Tag and Linker on RT Activity

To determine optimal properties of the tag and linker, the inventorsconstructed variants of the MalE-RF-TeI4c RT. The MalE-RT-TeI4c RT (leftbar) and variant proteins (right bars) were purified and assayed for RTactivity with poly(rA)/oligo(dT)₄₂ as described above (FIG. 13A).MalE-RT-TeI4c has a modified MalE tag (MalE (mod)) with 3 charged aminoacid residues changed to alanines and a linker of 5 alanine residueslinked to the N-terminus of the RT. Variants in which the 5alanine-residue linker was removed or shortened to 1 or 2 alanineresidues had substantial but reduced RT activity, as did a variant inwhich the modified MalE tag was replaced with wild-type MalE (MalE (WT))(FIG. 13A). A variant of TeI4c with the MalE (WT) tag followed by thepMal-c2t linker deleted for the TEV protease cleavage site also hadsubstantial but reduced RT activity (FIG. 13A). A variant in which thewild-type MalE tag was attached to the C-terminus of the TeI4c RT didnot express well in E. coli, presumably reflecting that the nascentTeI4c RT cannot fold properly without prior expression of the MalE tag.Finally, a variant with an N-terminal rigid fusion to NusA (Nutilization substance protein) instead of MalE had substantialthermostable RT activity (FIGS. 13A and B).

Temperature Profile for cDNA Synthesis

FIG. 14 shows assays of cDNA synthesis at different temperatures usingin vitro transcribed RNA templates with DNA primers annealed to their 3′ends comparing two of the thermostable group II intron RTs(MalE-RF-TeI4c and MalE-RF-GsI2) with a commercially available RT,SuperScript III (Invitrogen™), which has been reported to be active at55° C. (Potter et al. Focus (Invitrogen Newsletter) 25.1, 19-24, 2003).One template was a 531-nt in vitro transcript synthesized fromAflIII-digested pBS KS(+) with a ³²P-labeled 37-nt DNA primer annealed(FIG. 14A-C) and the other was a 1.2-kb kanR RNA (SEQ ID NO: 21; shownin FIG. 15) with a ³²P-labeled 44-nt DNA primer (FIG. 14D-E). Thereaction was incubated for 30 min at the indicated temperature, and theproducts were analyzed by electrophoresis in a denaturing 6%polyacrylamide gel. In each panel, the top and bottom autoradiogramsshow portions of the gel containing the full-length product andunextended or partially extended primers, respectively, and the bargraphs show the percentage of primer that was extended to full-lengthcDNA.

With the 531-nt RNA template, the MalE-RF-TeI4c RT had a temperatureoptimum for full-length cDNA synthesis of 61-81° C. The MalE-RF-GsI2 RTsynthesized full-length cDNA at temperatures between 37 and 69° C.,whereas SuperScript III RT had no activity at temperatures higher than57° C. (FIG. 14A-C). With the 1.2-kb RNA template, the MalE-RF-TeI4c andMalE-RF-GsI2 RT had temperature optima of 61-81° C. and 61-69° C.,respectively, while SuperScript III RT again had no activity attemperatures higher than 57° C. (FIG. 14D-E).

Analysis of cDNA Synthesis by qRT-PCR

In addition to gel analysis, the inventors used qRT-PCR to compare theamounts of cDNAs synthesized by the MalE-RF-TeI4c and SuperScript IIIRTs using the 1.2-kb RNA template. The inventors first compared theamounts of full-length cDNA produced at temperatures between 50 and 75°C. (FIG. 16). The cDNAs for qPCR were synthesized in reactionscontaining 5×10⁸ copies of kanR RNA as a template, 200 nM MalE-RT-TeI4cor 200 U of SuperScript III RT for 30 min at six different temperatures.Reactions with SuperScript III were done according to the manufacturer'sspecifications. The reaction mix containing all components except fordNTPs was preincubated at the desired temperatures for 2 min and startedby adding the dNTPs. After 30 min, the reactions were terminated byquickly freezing on dry ice. A 5-μl portion of each cDNA synthesis wasused in qPCR reactions containing TaqMan® Gene Expression mix and twoforward, reverse, and dual-labeled primer probe mixes located at nt188-257 and 562-634 of the kanamycin RNA. With the primer set closest tothe 5′ end of the RNA (nt 188-257), the cycle threshold (C_(T)) valueswere significantly lower for the MalE-RF-TeI4c RT than for SuperScriptIII RT at all temperatures tested (FIG. 16), indicating thatMalE-RF-TeI4c had synthesized larger amounts of cDNAs extending to nearthe 5′ end of the RNA template. Notably, the difference in amounts ofcDNAs synthesized was most pronounced at temperatures between 55 and 65°C., where the activity of SuperScript III falls off rapidly.

To compare the processivity of cDNA synthesis by MalE-RF-TeI4c andSuperScript III RTs, the same cDNA samples obtained at 60 and 65° C.were analyzed with two different amplicon primer/probe sets: 188-257,which detects cDNAs that are 920-nt long, and 562-634, which detectscDNAs that are 546 nt long (FIG. 17). In this case, cycle thresholdresults for cDNA samples were plotted against a standard curve obtainedwith Novagen® double-stranded DNA plasmid vector pET9a to determine copynumbers equivalents. With the 188-257 amplicon primer/probe set, 972,815copies were detected with the MalE-RF-4c TeI4c RT versus 64,456 copieswith SuperScript RT at 60° C. (˜15 fold difference), and that ratioincreased to 732,559 versus 661 at 65° C. (˜1100 fold difference).Further, at both temperatures, the MalE-RF-TeI4c RT shows littledifference in the copy numbers of cDNAs detected by the two primer sets,showing that the MalE-RF-TeI4c RT synthesizes mostly full-length cDNAs,indicative of high processivity. By contrast. SuperScript III RT showedlower numbers of longer cDNAs detected by the 188-257 primer set thanthe 562-634 primer set at both temperatures, indicating that this RTfalls off or is otherwise impeded before reaching the 5′ end of the RNA,resulting in synthesis of shorter cDNAs.

Fidelity of Nucleotide Incorporation by TeI4c and TeI4h* RTs

The inherent fidelity of the TeI4h* and TeI4c RTs (i.e., the nativegroup II intron RT, not a stabilized RT fusion protein) was assessedinitially by sequencing introns that had undergone retrohoming in E.coli plasmid assays (Table 2). The maximum error frequencies for theTeI4h* RNA promoting retrohoming of a TeI4h*-ΔORF intron RNA at 37 and48° C. were 1.6×10⁻⁵ and 4.1×10⁻⁶, respectively. The TeI4c RT is encodedby the outer intron of a “twintron”, a configuration in which one groupII intron (TeI3c) has inserted into another (TeI4c), and can efficientlymobilize both introns. The maximum error frequencies for the TeI4c RTpromoting retrohoming of TeI3c or TeI4c at 48° C. were 1.1×10⁻⁵ and2.2×10⁻⁵. These error frequencies are comparable to that estimatedpreviously for the Ll.LtrB intron RT (LtrA) promoting retrohoming of theLl.LtrB intron, ˜10⁻⁵ at 37° C. (Conlan et al., Nucl. Acids Res. 33,5262-5270, 2005).

TABLE 2 Fidelity of group II intron RTs as measured by frequency ofnucleotide misincorporation during retrohoming RT TeI4h* TeI4h* TeI4cTeI4c Intron TeI4h*-ΔORF TeI4h*-ΔORF TeI3c-ΔORF TeI4c-ΔORF Temp. 37 4848 48 (° C.) Nts 244,253 244,980 265,858 537,354 sequenced Mutations 4 13 12 Error 1.6 × 10⁻⁵ 4.1 × 10⁻⁶ 1.1 × 10⁻⁵ 2.2 × 10⁻⁵ Frequency

Retrohoming was done in E. coli HMS174(DE3) with donor plasmidsexpressing the indicated intron and RT and recipient plasmids containingthe intron target site (ligated E1-E2) sequences cloned upstream of apromoterless tet^(R) gene. After selection of Tet^(R) colonies, intronsthat had integrated into the target site in recipient plasmid wereamplified by colony PCR using the primers Rsense(5′-ACAAATAGGGGTTCCGCGCAC; SEQ ID NO: 22) and Te680rc(5′-GTTGGTGACCGCACCAGT; SEQ ID NO: 23) and Te420f (5′-AACGCGGTAAGCCCGTA;SEQ ID NO: 24) and Rev2pBRR (5′-AATGGACGATATCCCGCA; SEQ ID NO: 25) forthe 5′- and 3′-integration junctions, respectively. The PCR fragmentswere then sequenced. Table 2 indicates the induction temperature forretrohoming, the total number of intron nucleotides sequenced, thenumber of mutations (errors), and the error frequency.

The following examples of methods for preparing and characterizingstabilized RT fusion proteins are included for purposes of illustrationand are not intended to limit the scope of the invention.

EXAMPLES Example 1 Recombinant Plasmids

pMalE-TeI4c, pMalE-TeI4f, pMalE-TeI4h* contain the RT ORF of theindicated mobile group II intron with a fused N-terminal MalE tag clonedbehind the tac promoter in the expression vector pMal-c2t. The latter isa derivative of pMal-c2x (New England Biolabs, Ipswich Mass.) in whichthe factor Xa protease-cleavage site between MalE and the expressedprotein was replaced by a TEV protease-cleavage site (Kristelly et al.,Acta Crystallogr D Biol Crystallogr. 59, 1859-1862, 2003). The TeI4h* RTis a derivative of the native TeI4h RT with the YAGD motif in RT-5changed to YADD. Recombinant plasmids containing group II introns fromT. elongatus strain BP1 cloned in pET11 (TeI4f), pUC19 (TeI4c), orpACD2X (TeI4h*) were described previously. pMalE-RT plasmids werederived from these initial constructs by PCR amplifying the RT ORF withprimers that append restriction sites, and then cloning the PCR productsinto the corresponding sites of pMal-c2t (TeI4c RT, EcoRI and PstIsites; TeI4f RT, BamHI site; TeI4h* RT, BamHI and PstI sites).Recombinant plasmids denoted pMalE-RF-protein (e.g., pMalE-RF-TeI4c)were derived from the corresponding pMalE-RT plasmids by replacing theTEV-protease cleavable linker (TVDEALKDAQTNS₃N₁₀LENLYFQG; SEQ ID NO: 19)with a rigid linker (TVDAALAAAQTAAAAA; SEQ ID NO: 20) by the QuikChangePCR procedure using the Accuprime polymerase (Invitrogen, Makarova etal., BioTechniques 29, 970-972, 2000).

Derivatives of pMalE-RF-TeI4c with different linkers were constructed byPCR mutagenesis using the QuikChange procedure. The MalE tag was fusedto the C-terminus of the TeI4c ORF in pMal-c2L by amplifying the MalEsegment of pMal-c2t with primers that introduce a 5′ EcoRI site and a 3′PstI site, and the TeI4c ORF of pMalE-TeI4c with gene specific primersthat introduce a 5′ NdeI site and a 3′ EcoRI site, respectively, andcloning the fragments into pMal-c2t digested with NdeI and PstI.

pNusA-RF-TeI4c-His, which expresses the TeI4c RT with an N-terminal NusAtag fused to the protein via a rigid linker and a C-terminal His6 tag,was constructed by PCR amplifying the TeI4c RT ORF from pMAL-TeI4c withprimers that append SacII and KpnI sites and cloning the resulting PCRproduct between the corresponding sites of pET-50b(+) (Novagen). PCRmutagenesis was then used to replace the last two charged residues (Dand E) of NusA, the existing linker, and one of the two N-terminal His6tags (NICWFGDEATSGSGH₆; SEQ ID NO: 26) with a rigid linker sequence(NICWFGAAAAA; SEQ ID NO: 27). The second N-terminal His6 tag was removedby PCR mutagenesis and a His6 tag was fused to the C-terminus of TeI4cRT by QuikChange PCR.

pMalE-GsI1 and pMalE-GsI2 were constructed by PCR amplifying the RT ORFsfrom G. stearothermophilus strain 10 genomic DNA (obtained from GregDavis (Sigma-Aldrich)) by PCR with primers that amplify the introns andappended BamHI and XbaI sites (GsI1) or BamHI sites (GsI2) and thencloning the PCR products between the corresponding sites of pMal-c2t.GsI1 is a subgroup IIB2 intron that is inserted in the G.stearothermophilus recA gene and is related to the previously describedRT-encoding group 11 introns in the recA genes of Geobacilluskaustophilus (Chee et al., Gene 363, 211-220, 2005) and Bacilluscaldolyticus (Ng et al., Gene 393, 137-144, 2007). The cloned GsI1 RTORF was verified to correspond to the genomic sequence (CP001794). GsI2is a group IIC intron found in multiple copies in the G.stearothermophilus genome. The cloned GsI2 RT ORF corresponds to thegenomic sequence of one of six full-length copies of GsI2 in the G.stearothermophilus genome (CP001794) and has three amino acid sequencechanges from the RT ORF cloned by Vellore et al. (Appl. Environ.Microbiol. 70, 7140-7147, 2004). The corresponding pMalE-RF-RTconstructs were derived from the pMalE-RT constructs by QuikChange PCR,as described above.

pMalE-LtrA was constructed by PCR amplifying the LtrA ORF of pImp-2(Saldanha et al., Biochemistry 38, 9069-9083, 1999) using primers thatappend BamHI and HindIII sites and then cloning the PCR product betweenthe corresponding sites of pMal-c2t, and pMalE-RF-LtrA was derived frompMalE-LtrA by QuikChange PCR, as described above.

Example 2 Protein Purification

For expression of pMalE-RT or pMalE-RF-RT constructs, E. coli Rosetta2/pRARE (Novagen, EMD Biosciences, Gibbstown N.J.) or ScarabXpress/pRARET7lac (Scarabgenomics, Madison Wis.) were transformed with theexpression plasmid and grown at 37° C. in TB or LB medium to mid-logphase (O.D.₆₀₀=0.8). Expression was induced either by adding isopropylβ-D-1-thiogalactopyranoside (IPTG; 1 mM final) to mid-log phase cells(pMalE-RF-TeI4c, TeI4f, TeI4h*, GsI1, and GsI2) or by growing cells inauto-induction medium (LB containing 0.2% lactose, 0.05% glucose, 0.5%glycerol, 24 mM (NH₄)₂SO₄, 50 mM KH₂PO₄, 50 mM Na₂HPO₄) (pMalE-LtrA andpMalE-RF-LtrA). In either case, induction was for ˜24 h at 18-25° C.,after which cells were pelleted by centrifugation, resuspended in bufferA (20 mM Tris-HCl, pH 7.5, 0.5 M KCl or NaCl, 1 mM EDTA, 1 mMdithiothreitol (DTT)), and frozen at −80° C.

For purification of MalE-RF-TeI4c, TeI4f, TeI4h* and their derivatives,the cell suspension was thawed, treated with lysozyme (1 mg/ml; Sigma)for 15 min on ice, freeze-thawed three times on dry ice, sonicated(Branson 450 Sonifier, Branson Ultrasonics, Danbury Conn.) three or four10 sec bursts or one 30 sec burst on ice at an amplitude of 60%, with 10sec between bursts, and centrifuged for 30 min at 18,500×g at 4° C.Nucleic acids were precipitated by adding polyethyleneimine (PEI) to afinal concentration of 0.1% and centrifuging for 15 min at 15,000×g at4° C. in a J16.25 rotor in an Avanti J-E centrifuge (Beckman Coulter,Brea Calif.). The resulting supernatant was applied to an amylose column(10-ml column volume; Amylose High-Flow (New England Biolabs),equilibrated in buffer A), which was washed with five column volumeseach of buffer A containing 0.5 M, 1.5 M, or 0.5 M KCl, and then elutedwith buffer A containing 10 mM maltose. Protein fractions were pooledand purified further via a heparin-Sepharose column (3 tandem 1-mlcolumns; GE Healthcare Biosciences Corp.) which had beenpre-equilibrated in 20 mM Tris-HCl, pH 7.5 containing KCl (100 mM forMalE-RF-4c, 4f, 4h*, MalE-LtrA and MalE-RF-LtrA; 50 mM for MalE-RF-GsI1or GsI2), 1 mM EDTA, 1 mM DTT, 10% glycerol. The proteins were appliedto the column in the same buffer and eluted with a 40-column volumegradient from the loading concentration to 2 M KCl. The proteins elutedat ˜800 mM KCl. The peak fractions were pooled and dialyzed against 20mM Tris-HCl, pH 7.5, 0.5 M KCl, 1 mM EDTA, 1 mM DTT, and 50% glycerolfor storage. The frozen proteins showed no decrease in RT activity forat least six months.

The MalE-RF-GsI1 protein, which has an N-terminal MalE tag and aC-terminal His6-tag, was purified similarly, except that nucleic acidswere precipitated with 0.2% PEI, and the protein eluted from the amylosecolumn was purified further on a nickel column prior to the finalheparin-Sepharose column. The nickel column (5 ml HisTrap™ HP NickelSepharose; GE Healthcare Biosciences, Piscataway N.J.) equilibrated withbinding buffer (500 mM KCl, 20 mM Tris-HCl pH 7.5, 40 mM imidazole, and10% glycerol) was loaded with pooled protein fractions from the amylosecolumn, washed with 10 column volumes of binding buffer, eluted withfive column volumes of elution buffer (500 mM KCl, 20 mM Tris-HCl pH7.5, 400 mM imidazole and 10% glycerol), and the supernatant loadeddirectly onto the heparin-Sepharose column. The peak fractions from theheparin-Sepharose column were pooled, dialyzed against 20 mM Tris-HCl,pH 7.5, 0.5 M KCl, 50% glycerol, and stored as described above.

For the NusA fusions, E. coli ScarabXpress/pRARE T7lac cells wereinduced with 0.5 mM IPTG for 48 h at 18° C. and resuspended in nickelbuffer A (20 mM Tris pH 7.5, 500 mM KCl, 30 mM imidazole, 10% glycerol).After disrupting the cells as described above, nucleic acids wereprecipitated from the lysate by adding a final concentration of 0.2%polyethyleneimine, followed by centrifugation at 10.000×g for 15 min.The supernatant was applied to a 5-ml nickel-Sepharose columnpre-equilibrated with nickel buffer A, and then eluted with nickelbuffer A containing 500 mM imidazole. The protein fractions were pooledand loaded directly onto two connected 1-ml heparin-Sepharose columnsthat had been pre-equilibrated in 20 mM Tris pH 7.5, 100 mM KCl, 1 mMDTT, 1 mM EDTA, and 20% glycerol. The protein was eluted with a20-column volume gradient of 0.1 to 1.5 M KCl, and peak fractions werepooled, dialyzed against 20 mM Tris-HCl, pH 7.5, 0.5 M KCl, 1 mM EDTA, 1mM DTT, 50% glycerol, and stored as described above.

Example 3 Reverse Transcriptase Assays

RT activity at different temperatures was assayed by quantifyingincorporation of ³²P-dTTP using poly(rA)/oligo(dT)₄₂ as thetemplate-primer. The RT (50 nM MalE-RF-TeI4c RT or 100 nM of all otherRTs) was pre-incubated with 100 nM poly(rA)/oligo(dT)₄₂ in 1×RT buffer(75 mM KCl, 10 mM MgCl₂, 20 mM Tris-HCl, pH 7.5, and 1 mM DTT) atdifferent temperatures (ranging from 25-77° C.), and reactions wereinitiated by adding 5 μCi [α-³²P]-dTTP (3,000 Ci/mmol; Perkin Elmer,Waltham Mass.). The reactions were incubated for Limes within the linearrange and stopped by adding EDTA to a final concentration of 250 mM.Reaction products were spotted onto Whatman DE81 chromatography paper(10×7.5-cm sheets; GE Healthcare), washed 3 times in 0.3 M NaCl and 0.03M sodium citrate, and scanned with a PhosphorImager (Typhoon TrioVariable Mode Imager; GE Healthcare) to quantify bound radioactivity.

Other RT assays used RNA templates with annealed DNA oligonucleotideprimers. The RNA template was either a 531-nt in vitro transcriptsynthesized from pBluescript KS (+) digested with AflIII transcribedusing T7 Megscript kits (Ambion, Applied Biosystems, Austin, Tex.) or a1.2-kb kanR RNA purchased from Promega (Promega, Madison Wis.). In vitrotranscription was done according to the manufacturer's instructions for4 h at 37° C. After digesting the DNA template with Turbo DNase I (5min, 37° C.), RNAs were extracted with phenol:chloroform:isoamyl alcohol(25:24:1; phenol-CIA) and purified by two cycles of gel filtrationthrough Sephadex G-50 (Sigma, St Louis, Mo.) spin columns. The RNAconcentration was determined by using a Nanodrop (Thermo Scientific,Wilmington, Del.). RNAs were stored in Milli-Q-grade H₂O and stored at−20° C.

DNA oligonucleotide primers complementary to the 3′ ends of the RNAswere synthesized by IDT (Coralville, Iowa; AflIII primer:5′-CCGCCTTIGAGTGAGCTGATACCGCTCGCCGCAGCCG; SEQ ID NO: 28: P078 KanamycinRev 5′-GGTGGACCAGTTGGTGATITGAACTITTIGCTTGCCACGGAAC; SEQ ID NO: 29).Primer concentrations were determined by A₂₆₀. The primers were 5′³²P-labeled with T4 polynucleotide kinase (New England Biolabs)according to the manufacturer's instructions, and free nucleotides wereremoved by gel filtration through a Sephadex G-25 column. The primerswere mixed with the template at a molar ratio of 1.0:1.1 and annealed byheating to 82° C. for 2 min and then cooling to room temperature in aGeneAmp 9700 PCR cycler with the ramp setting of 10%.

For gel analysis of cDNA synthesis, 100 nM of annealed template/primerwas incubated with 200 nM enzyme in 100 mM KCl, 20 mM Tris HCl pH 7.5,10 mM MgCl₂ and 1 mM DTT for MalE-RF-TeI4c RT and in 10 mM NaCl, 20 mMTris HCl pH 7.5, 10 mM MgCl₂ and 1 mM DTT for MalE-RF-GsI2 RT. Reactionswere initiated by adding dNTPs and MgCl₂ to final concentrations of 1.25mM and 10 mM, respectively, incubated for 30 min at the indicatedtemperature, and terminated by adding 0.1% SDS/250 mM EDTA (finalconcentrations) followed by phenol-CIA extraction. The products wereanalyzed by electrophoresis in a denaturing 6% polyacrylamide gel, whichwas dried and quantified with a PhosphorImager. A 5′-labeled 10-bpladder (Invitrogen™) was used as size markers.

Example 4 Quantitative Real-Time Polymerase Chain Reaction (qPCR)

cDNAs for qPCR analysis were generated in 20 μl reactions containing1×RT buffer (75 mM KCl, 10 mM MgCl₂, 20 mM Tris-HCl, pH 7.5), 1 mM DTT,5×10⁸ copies of kanR RNA, 200 nM MalE-RF-TeI4c RT and 1 mM dNTPs for 30min at temperatures specified for individual experiments. Parallelreactions with SuperScript III (Invitrogen) were done according to themanufacturers specifications. Reactions were incubated at the differenttemperatures for 2 min and started by adding dNTPs. After incubating for30 min, the reactions were quickly frozen on dry ice to stop thereactions. 5 μl of cDNA reaction were used for the qPCR.

qPCR analysis was done in 96-well plates with optical caps with eachwell containing 25 μl of reaction mix consisting of 12.5 μl of 2×TaqMan® Gene Expression Master Mix (Applied Biosystems, Foster City,Calif.), 7.5 μl of forward, reverse, and dual-labeled probe mix(oligonucleotides purchased individually from Integrated DNATechnologies, Coralville, Iowa), and 5 μl cDNA template. The mixture wasincubated in the 7900HT Fast Real-Time PCR System (Applied Biosystems),using the 9600 emulation mode protocol (50° C. for 2 min, 95° C. for 10min, then cycled for a total of 45 cycles at 95° C. for 15 sec and 60°C. for 60 sec). Data were collected and analyzed using the AppliedBiosystems Sequence Detection System Software, Versions 2.2 or 2.3.

The Novagen® double-stranded DNA plasmid vector pET9a (EMD Chemicals)was used to quantitate kanR cDNA levels. The pET9a vector contains thekanR coding sequence (bases 3523-4335) and has 100% sequence homology ateach primer/probe binding site with the Promega 1.2-kb kanR RNA.Purified and quantitated pET9a DNA vector was initially diluted to 1×10⁹copies/μl stock aliquots and stored at −20° C. For each run, freshstocks were thawed and then serially diluted to generate a quantitativestandard curve used in qPCR. Cycle threshold results for cDNA sampleswere then plotted against the standard curve to determine copy numbersequivalents.

Primers used were:

P078 Kanamycin RT-1107R SEQ ID NO: 295′-GGTGGACCAGTTGGTGATTTTGAACTTTTGCTTTGCCA CGGAAC-3′; (Tm = 80° C.)primer sets nt 188-257: Forward- P029 kan-188F: SEQ ID NO: 305′-GGGTATAAATGGGCTCGCG-3′; Reverse- P030 kan-257R: SEQ ID NO: 315′-CGGGCTTCCCATACAATCG-3′; Taqman Probe- P031 kan-213T: SEQ ID NO: 325′(6-carboxyfluorescein(6FAM))-TCGGGCAATC AGGTGCGACAATC-3′;(Iowa Black FQ; a dark non-fluorescent quencher); Amplicon 70 bp:SEQ ID NO: 33 5′GGGTATAAATGGGCTCGCGATAATGTCGGGCAATCAGGTGCGACAATCTATCGATTGTATGGGAGCCCG-3′; Primer Set (nt 562-634):Forward- P001 kan-562R: SEQ ID NO: 34 5′-CGCTCAGGCGCAATCAC-3′;Reverse- P002 kan-634R: SEQ ID NO: 35 5′-CCAGCCATTACGCTCGTCAT-3′;Taqman Probe- P003 kan-581T: SEQ ID NO: 365′(6-FAM)-ATGAATAACGGTTTGGTTGATGCGAGT GA-3′-(TAMRA); Amplicon 73 bpSEQ ID NO: 37 5′CGCTCAGGCGCAATCACGAATGAATAACGGTTTGGTTGATGCGAGTGATTTTGATGACGAGCGTAATGGCTGG-3′;

Example 5 Retrohoming Assays

Retrohoming assays were done in E. coli HMS174(DE3) (Novagen™) grown onLB medium, with antibiotics added at the following concentrations:ampicillin, 100 μg/ml; chloramphenicol, 25 μg/ml; tetracycline, 25μg/ml. The intron-donor plasmids, derivatives of pACD2X (San Filippo etal., Journal of Molecular Biology, 324, 933-951, 2002), carry a cap^(R)marker and use a T7lac promoter to express a ΔORF intron (I-ΔORF) withshort flanking 5′ and 3′ exons (E1 and E2, respectively) and a T7promoter in DIV, followed by the RT ORF downstream of E2. The recipientplasmids, derivatives of pBRR-tet (Guo et al., Science 289, 452-457,2000; Karberg et al., Nature Biotech. 19, 1162-1167, 2001), carry anamp^(R) marker and contain a target site for the intron (ligated E1-E2sequences) cloned upstream of a promoterless tet^(R) gene. The latter isactivated by insertion of the intron carrying the T7 promoter, enablingselection for Tet^(R)+Amp^(R) colonies. For the assays, cells wereco-transformed with the Cap^(R) donor and Amp^(R) recipient plasmids,inoculated into 5 ml of LB medium containing chloramphenicol andampicillin, and grown with shaking (200 rpm) overnight at 37° C. A smallportion (50 μl) of the overnight culture was inoculated into 5 ml offresh LB medium containing the same antibiotics and grown for 1 h asabove. The cells were then induced with IPTG for 1 h under conditionsspecified in the legend of Table 1 for individual experiments. Thecultures were then placed on ice, diluted with ice-cold LB, and platedat different dilutions onto LB agar containing ampicillin orampicillin+tetracycline. After incubating the plates overnight at 37°C., the mobility efficiency was calculated as the ratio of(Tet^(R)+Amp^(R))/Amp^(R) colonies.

1-25. (canceled)
 26. A method of stabilizing a reverse transcriptase,comprising connecting a soluble stabilizer protein to a reversetranscriptase to form a stabilized reverse transcriptase fusion protein,and using the stabilized reverse transcriptase fusion protein to carryout reverse transcription.
 27. The method of claim 26, wherein thereverse transcriptase is a thermostable reverse transcriptase.
 28. Themethod of claim 27, wherein the thermostable reverse transcriptase is abacterial thermostable reverse transcriptase.
 29. The method of claim28, wherein the bacterial thermostable reverse transcriptase is aThermosynechococcus elongatus reverse transcriptase or a Geobacillusstearothermophilus reverse transcriptase.
 30. The method of claim 26,wherein the reverse transcriptase is a group-II intron-derived reversetranscriptase.
 31. The method of claim 26, wherein the reversetranscriptase comprises a polypeptide having at least 85% amino acidsequence identity to a sequence selected from the group consisting ofSEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, or SEQ ID NO: 5.32. The method of claim 26, wherein the stabilized reverse transcriptasefusion protein comprises an amino acid sequence with at least 85% aminoacid sequence identity to a sequence selected from the group consistingof SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, or SEQ ID NO:10.
 33. The method of claim 26, wherein the soluble stabilizer proteincomprises an affinity protein or a solubility enhancing protein.
 34. Themethod of claim 33, wherein the soluble stabilizer protein comprises amaltose binding protein or an N-utilization substance A protein.
 35. Themethod of claim 26, wherein the soluble stabilizer protein includes 50or more amino acids.
 36. The method of claim 26, wherein the solublestabilizer protein does not fold into long-lived misfoldedintermediates.
 37. The method of claim 26, wherein the reversetranscriptase is connected to the soluble stabilizer protein by a linkerpeptide.
 38. The method of claim 37, wherein the linker peptide is anon-cleavable linker peptide.
 39. The method of claim 37, wherein thelinker peptide is a rigid linker peptide.
 40. The method of claim 26,wherein the reverse transcription is carried out with an error frequencyof 2.0×10⁻⁵ or less at a temperature from about 45° to about 65° C. 41.A method for preparing a cDNA from an RNA molecule, comprising the stepsof: (a) adding a primer nucleotide sequence to the RNA molecule (b)incubating the RNA molecule in the presence of one or more deoxy ordideoxyribonucleoside triphosphates and a stabilized reversetranscriptase fusion protein comprising a reverse transcriptaseconnected to a soluble stabilizer protein under conditions sufficient tosynthesize a cDNA molecule complementary to all or a portion of the RNAmolecule.
 42. The method of claim 41, wherein the reverse transcriptaseis connected to the stabilizer protein by a non-cleavable linkerpeptide.
 43. The method of claim 41, wherein reverse transcription isperformed within a temperature range where the RNA has a substantiallydecreased amount of obstructing stable secondary or tertiary structure.44. The method of claim 41, wherein the reverse transcriptase is agroup-II intron-derived reverse transcriptase.
 45. A DNA expressionvector for producing a stabilized reverse transcriptase fusion protein,comprising an isolated nucleic acid that encodes a polypeptide with atleast 85% amino acid sequence identity to a sequence selected from thegroup consisting of SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO:9, or SEQ ID NO:
 10. 46. A method of producing a stabilized reversetranscriptase fusion protein, comprising the steps of (a) culturing ahost cell comprising the DNA expression vector of claim 45; (b)expressing the stabilized reverse transcriptase fusion protein encodedby the DNA expression vector; and (c) isolating the stabilized reversetranscriptase fusion protein from the host cell.